Multiple sequence alignment - TraesCS6D01G142100

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6D01G142100 chr6D 100.000 4414 0 0 1 4414 111571051 111566638 0.000000e+00 8152.0
1 TraesCS6D01G142100 chr6D 79.845 387 56 10 268 637 176487494 176487875 3.390000e-66 263.0
2 TraesCS6D01G142100 chr6D 95.370 108 2 3 4308 4414 352086755 352086650 7.590000e-38 169.0
3 TraesCS6D01G142100 chr6A 88.535 2477 168 43 1 2400 136540487 136542924 0.000000e+00 2894.0
4 TraesCS6D01G142100 chr6A 88.638 1593 112 30 2461 4027 136543258 136544807 0.000000e+00 1875.0
5 TraesCS6D01G142100 chr6A 81.788 302 48 7 423 721 474994884 474995181 3.410000e-61 246.0
6 TraesCS6D01G142100 chr6B 92.614 1882 67 28 2481 4312 200510014 200508155 0.000000e+00 2639.0
7 TraesCS6D01G142100 chr6B 96.982 1458 29 6 1016 2466 200512034 200510585 0.000000e+00 2435.0
8 TraesCS6D01G142100 chr6B 88.900 1009 69 11 2 981 200513027 200512033 0.000000e+00 1203.0
9 TraesCS6D01G142100 chr4D 81.081 555 67 18 152 692 39393271 39392741 4.110000e-110 409.0
10 TraesCS6D01G142100 chr4D 78.912 147 23 3 3878 4023 101625763 101625902 4.700000e-15 93.5
11 TraesCS6D01G142100 chr7D 78.306 673 115 17 85 727 617207101 617206430 5.320000e-109 405.0
12 TraesCS6D01G142100 chr7D 78.041 633 94 33 85 697 98984831 98985438 1.510000e-94 357.0
13 TraesCS6D01G142100 chr7D 79.435 496 64 18 145 627 567516091 567515621 2.560000e-82 316.0
14 TraesCS6D01G142100 chr7D 80.000 340 60 6 429 764 236834217 236834552 1.230000e-60 244.0
15 TraesCS6D01G142100 chr7D 84.259 108 12 4 2137 2239 592633551 592633658 2.810000e-17 100.0
16 TraesCS6D01G142100 chr7D 92.727 55 4 0 87 141 171374890 171374944 3.660000e-11 80.5
17 TraesCS6D01G142100 chr1D 80.289 553 84 15 147 693 38368990 38369523 1.150000e-105 394.0
18 TraesCS6D01G142100 chr1D 78.216 583 87 17 147 704 426890081 426890648 1.970000e-88 337.0
19 TraesCS6D01G142100 chr1D 81.661 289 52 1 433 720 332959027 332959315 5.710000e-59 239.0
20 TraesCS6D01G142100 chr1D 91.209 91 2 6 1 87 83479075 83479163 7.760000e-23 119.0
21 TraesCS6D01G142100 chr3D 78.537 629 84 18 85 683 407219578 407218971 2.510000e-97 366.0
22 TraesCS6D01G142100 chr3D 77.484 644 112 23 85 704 522296279 522296913 5.430000e-94 355.0
23 TraesCS6D01G142100 chr3D 95.370 108 2 3 4308 4414 472075297 472075192 7.590000e-38 169.0
24 TraesCS6D01G142100 chr3D 76.630 184 29 10 407 582 570526450 570526273 6.080000e-14 89.8
25 TraesCS6D01G142100 chr2B 77.882 642 106 21 85 693 26358790 26358152 2.510000e-97 366.0
26 TraesCS6D01G142100 chr2B 76.947 642 112 17 85 693 26392543 26391905 2.540000e-87 333.0
27 TraesCS6D01G142100 chr2B 98.000 100 2 0 4315 4414 183936983 183936884 1.630000e-39 174.0
28 TraesCS6D01G142100 chr2B 87.850 107 9 4 1600 1706 725579757 725579655 6.000000e-24 122.0
29 TraesCS6D01G142100 chr2B 93.421 76 4 1 16 90 685766919 685766844 1.300000e-20 111.0
30 TraesCS6D01G142100 chr2B 88.421 95 6 5 3 94 377319819 377319911 4.670000e-20 110.0
31 TraesCS6D01G142100 chr7B 78.667 525 90 12 186 693 732154726 732155245 3.290000e-86 329.0
32 TraesCS6D01G142100 chr7B 75.610 615 106 21 85 667 627616762 627617364 9.410000e-67 265.0
33 TraesCS6D01G142100 chr7B 75.382 654 103 21 85 695 521201560 521202198 3.390000e-66 263.0
34 TraesCS6D01G142100 chr7B 92.683 82 5 1 1 81 510055557 510055638 2.790000e-22 117.0
35 TraesCS6D01G142100 chr7B 78.689 183 27 7 3877 4051 699358196 699358374 1.300000e-20 111.0
36 TraesCS6D01G142100 chrUn 76.489 638 99 25 85 683 32258573 32257948 2.580000e-77 300.0
37 TraesCS6D01G142100 chr3B 84.470 264 41 0 145 408 128678321 128678584 1.220000e-65 261.0
38 TraesCS6D01G142100 chr3B 80.282 284 39 11 85 352 525380695 525380977 9.680000e-47 198.0
39 TraesCS6D01G142100 chr3B 91.011 89 7 1 1 88 596864485 596864573 7.760000e-23 119.0
40 TraesCS6D01G142100 chr7A 82.353 306 31 16 1444 1748 685213048 685213331 1.230000e-60 244.0
41 TraesCS6D01G142100 chr2A 78.205 390 64 8 322 696 16777921 16777538 3.430000e-56 230.0
42 TraesCS6D01G142100 chr2A 95.370 108 2 3 4308 4414 525895667 525895562 7.590000e-38 169.0
43 TraesCS6D01G142100 chr2A 91.398 93 7 1 1600 1692 730616887 730616796 4.630000e-25 126.0
44 TraesCS6D01G142100 chr5A 96.296 108 1 3 4308 4414 155040080 155039975 1.630000e-39 174.0
45 TraesCS6D01G142100 chr5A 95.370 108 2 3 4308 4414 358435531 358435426 7.590000e-38 169.0
46 TraesCS6D01G142100 chr3A 96.262 107 3 1 4308 4414 293403647 293403752 1.630000e-39 174.0
47 TraesCS6D01G142100 chr5D 95.370 108 2 3 4308 4414 243456856 243456751 7.590000e-38 169.0
48 TraesCS6D01G142100 chr5D 77.512 209 33 6 3876 4083 350227239 350227434 3.610000e-21 113.0
49 TraesCS6D01G142100 chr5D 87.500 72 7 2 3878 3947 464006848 464006919 1.020000e-11 82.4
50 TraesCS6D01G142100 chr1A 95.370 108 2 3 4308 4414 147500416 147500311 7.590000e-38 169.0
51 TraesCS6D01G142100 chr1A 90.805 87 6 2 1 86 451380681 451380596 1.000000e-21 115.0
52 TraesCS6D01G142100 chr2D 91.398 93 7 1 1600 1692 596553600 596553509 4.630000e-25 126.0
53 TraesCS6D01G142100 chr2D 92.683 82 5 1 1 81 266507406 266507325 2.790000e-22 117.0
54 TraesCS6D01G142100 chr2D 94.737 57 3 0 85 141 603917571 603917515 6.080000e-14 89.8
55 TraesCS6D01G142100 chr4B 92.593 81 5 1 1 81 96706357 96706278 1.000000e-21 115.0
56 TraesCS6D01G142100 chr1B 77.305 141 20 9 634 763 338005095 338005234 6.120000e-09 73.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G142100 chr6D 111566638 111571051 4413 True 8152.000000 8152 100.0000 1 4414 1 chr6D.!!$R1 4413
1 TraesCS6D01G142100 chr6A 136540487 136544807 4320 False 2384.500000 2894 88.5865 1 4027 2 chr6A.!!$F2 4026
2 TraesCS6D01G142100 chr6B 200508155 200513027 4872 True 2092.333333 2639 92.8320 2 4312 3 chr6B.!!$R1 4310
3 TraesCS6D01G142100 chr4D 39392741 39393271 530 True 409.000000 409 81.0810 152 692 1 chr4D.!!$R1 540
4 TraesCS6D01G142100 chr7D 617206430 617207101 671 True 405.000000 405 78.3060 85 727 1 chr7D.!!$R2 642
5 TraesCS6D01G142100 chr7D 98984831 98985438 607 False 357.000000 357 78.0410 85 697 1 chr7D.!!$F1 612
6 TraesCS6D01G142100 chr1D 38368990 38369523 533 False 394.000000 394 80.2890 147 693 1 chr1D.!!$F1 546
7 TraesCS6D01G142100 chr1D 426890081 426890648 567 False 337.000000 337 78.2160 147 704 1 chr1D.!!$F4 557
8 TraesCS6D01G142100 chr3D 407218971 407219578 607 True 366.000000 366 78.5370 85 683 1 chr3D.!!$R1 598
9 TraesCS6D01G142100 chr3D 522296279 522296913 634 False 355.000000 355 77.4840 85 704 1 chr3D.!!$F1 619
10 TraesCS6D01G142100 chr2B 26358152 26358790 638 True 366.000000 366 77.8820 85 693 1 chr2B.!!$R1 608
11 TraesCS6D01G142100 chr2B 26391905 26392543 638 True 333.000000 333 76.9470 85 693 1 chr2B.!!$R2 608
12 TraesCS6D01G142100 chr7B 732154726 732155245 519 False 329.000000 329 78.6670 186 693 1 chr7B.!!$F5 507
13 TraesCS6D01G142100 chr7B 627616762 627617364 602 False 265.000000 265 75.6100 85 667 1 chr7B.!!$F3 582
14 TraesCS6D01G142100 chr7B 521201560 521202198 638 False 263.000000 263 75.3820 85 695 1 chr7B.!!$F2 610
15 TraesCS6D01G142100 chrUn 32257948 32258573 625 True 300.000000 300 76.4890 85 683 1 chrUn.!!$R1 598

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
766 895 0.693049 ACGGATTTGAGGTGCCTCTT 59.307 50.000 17.96 4.57 43.12 2.85 F
980 1126 1.338200 GCGTCACCACCTTTCTCATCT 60.338 52.381 0.00 0.00 0.00 2.90 F
1978 2153 1.135083 GTACCACTAGCACGCACATCT 60.135 52.381 0.00 0.00 0.00 2.90 F
2318 2495 2.480416 GCGATCACAGGAGTAAGACCAG 60.480 54.545 0.00 0.00 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1978 2153 0.249238 GAACACCATTGCAACGCCAA 60.249 50.0 0.00 0.00 0.00 4.52 R
2081 2256 0.392998 CACAGAACCGGATCTTGGGG 60.393 60.0 12.21 3.33 0.00 4.96 R
3050 4084 0.299895 CGTTGTCGATCTCATGCTGC 59.700 55.0 0.00 0.00 39.71 5.25 R
4267 5342 1.081892 CACGAGGTCCTTGCTTCATG 58.918 55.0 5.98 0.00 0.00 3.07 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
302 319 3.439540 CACCATTTGGGCGGACGG 61.440 66.667 0.96 0.00 42.05 4.79
386 405 2.280524 CACAAGCCGGACGACCAA 60.281 61.111 5.05 0.00 35.59 3.67
387 406 1.890041 CACAAGCCGGACGACCAAA 60.890 57.895 5.05 0.00 35.59 3.28
443 500 3.082579 GCAGGACTCGGATCCGCTT 62.083 63.158 29.62 17.91 44.22 4.68
704 833 1.336517 CCCGTTTGAAGCGTCTGTCTA 60.337 52.381 0.31 0.00 0.00 2.59
705 834 2.400399 CCGTTTGAAGCGTCTGTCTAA 58.600 47.619 0.31 0.00 0.00 2.10
721 850 7.957484 CGTCTGTCTAAATCGAATTTTTGTGAT 59.043 33.333 0.00 0.00 33.82 3.06
728 857 3.403968 TCGAATTTTTGTGATCGGACCA 58.596 40.909 0.00 0.00 36.05 4.02
732 861 2.869101 TTTTGTGATCGGACCATCCA 57.131 45.000 0.00 0.00 35.91 3.41
740 869 3.118454 GGACCATCCACACACGCG 61.118 66.667 3.53 3.53 36.28 6.01
766 895 0.693049 ACGGATTTGAGGTGCCTCTT 59.307 50.000 17.96 4.57 43.12 2.85
810 948 1.463056 CGTTTGCGCAGATAAAGGACA 59.537 47.619 11.31 0.00 0.00 4.02
980 1126 1.338200 GCGTCACCACCTTTCTCATCT 60.338 52.381 0.00 0.00 0.00 2.90
1407 1553 2.347490 GCTGGGTTCCTGAAGCGA 59.653 61.111 3.28 0.00 39.53 4.93
1978 2153 1.135083 GTACCACTAGCACGCACATCT 60.135 52.381 0.00 0.00 0.00 2.90
2023 2198 7.660617 CGATCAGATACCTAAACCTACTCTGTA 59.339 40.741 0.00 0.00 32.49 2.74
2045 2220 2.856557 CAGACTGCAGATACATGACGTG 59.143 50.000 23.35 0.00 0.00 4.49
2046 2221 2.493675 AGACTGCAGATACATGACGTGT 59.506 45.455 23.35 5.47 44.95 4.49
2047 2222 3.694566 AGACTGCAGATACATGACGTGTA 59.305 43.478 23.35 9.90 46.73 2.90
2048 2223 4.033990 ACTGCAGATACATGACGTGTAG 57.966 45.455 23.35 2.89 45.94 2.74
2049 2224 3.181486 ACTGCAGATACATGACGTGTAGG 60.181 47.826 23.35 6.61 45.94 3.18
2050 2225 3.020984 TGCAGATACATGACGTGTAGGA 58.979 45.455 12.83 0.00 45.94 2.94
2096 2271 5.952347 ATATATACCCCAAGATCCGGTTC 57.048 43.478 0.00 1.92 0.00 3.62
2318 2495 2.480416 GCGATCACAGGAGTAAGACCAG 60.480 54.545 0.00 0.00 0.00 4.00
2447 2855 2.951229 ACCTCCCGAAACTTTGTCAT 57.049 45.000 0.00 0.00 0.00 3.06
2450 2858 2.504367 CTCCCGAAACTTTGTCATGGT 58.496 47.619 0.00 0.00 0.00 3.55
2470 2921 9.337396 TCATGGTTTAGCGAGTATTTTAATGAT 57.663 29.630 0.00 0.00 0.00 2.45
2508 3515 4.382306 ACAACAACAAAAACTGTTTGCG 57.618 36.364 6.53 3.78 46.49 4.85
2519 3526 6.806120 AAAACTGTTTGCGTAATTCTCAAC 57.194 33.333 6.53 0.00 0.00 3.18
2729 3752 9.964354 TTGGATAGAAAGTAGTAGTAGTACACA 57.036 33.333 15.89 0.00 0.00 3.72
2766 3789 7.770897 CCTAGATGCTACTTCTACATTTTGGTT 59.229 37.037 0.00 0.00 0.00 3.67
3149 4183 4.421479 CCGCCTCAAGACGACGCT 62.421 66.667 0.00 0.00 0.00 5.07
3215 4249 2.515071 GCCCGATGAGCAGGAGGAT 61.515 63.158 0.00 0.00 0.00 3.24
3219 4253 0.319727 CGATGAGCAGGAGGATGAGC 60.320 60.000 0.00 0.00 0.00 4.26
3226 4260 1.993948 AGGAGGATGAGCAGCAGCA 60.994 57.895 3.17 0.00 45.49 4.41
3227 4261 1.524165 GGAGGATGAGCAGCAGCAG 60.524 63.158 3.17 0.00 45.49 4.24
3228 4262 2.124653 AGGATGAGCAGCAGCAGC 60.125 61.111 3.17 0.46 45.49 5.25
3344 4390 3.774959 ATCGGATCAGCGTCGCCAC 62.775 63.158 14.86 2.85 0.00 5.01
3448 4494 3.699413 TCCATTGCATGAATGAACCTGA 58.301 40.909 15.30 5.26 43.87 3.86
3533 4579 2.694628 AGAAAACAAGCTGGTTGCATGA 59.305 40.909 18.64 0.00 42.37 3.07
3546 4592 1.077501 GCATGAACTAGGCTGGGCA 60.078 57.895 2.02 0.18 32.24 5.36
3547 4593 0.466922 GCATGAACTAGGCTGGGCAT 60.467 55.000 2.02 2.78 32.24 4.40
3618 4666 6.495526 TCCCGATTTAATTTCCTGACCTTTTT 59.504 34.615 0.00 0.00 0.00 1.94
3625 4673 4.654091 TTTCCTGACCTTTTTCTGCTTG 57.346 40.909 0.00 0.00 0.00 4.01
3650 4698 9.646427 TGCTGTGTTTTTAATTGTACTTTTCTT 57.354 25.926 0.00 0.00 0.00 2.52
3786 4852 9.341899 CCATGTTTTGTTTCTTTACTAGTATGC 57.658 33.333 2.79 0.00 0.00 3.14
3822 4892 8.792633 CAAACTTGTTGAGGATTCTAATGGTTA 58.207 33.333 0.00 0.00 0.00 2.85
3874 4944 5.702865 ACAGCTATATGTTGTTGCAAAGTG 58.297 37.500 0.00 0.00 36.73 3.16
3903 4973 3.943381 CCCTTCGGTTGGGTTTATAAGTC 59.057 47.826 0.00 0.00 39.82 3.01
3904 4974 4.324022 CCCTTCGGTTGGGTTTATAAGTCT 60.324 45.833 0.00 0.00 39.82 3.24
3987 5062 7.969387 AAATATTTGGATTCGTCGTCAAATG 57.031 32.000 18.66 0.00 39.32 2.32
4052 5127 6.208599 GGTTCATTAGTCAAATCAAAGACCCA 59.791 38.462 0.00 0.00 35.38 4.51
4058 5133 5.670485 AGTCAAATCAAAGACCCAAAAACC 58.330 37.500 0.00 0.00 35.38 3.27
4061 5136 5.188751 TCAAATCAAAGACCCAAAAACCTGT 59.811 36.000 0.00 0.00 0.00 4.00
4083 5158 2.643801 ACCCGACTAATAAACCCAACCA 59.356 45.455 0.00 0.00 0.00 3.67
4094 5169 4.302559 AAACCCAACCAGAGGAGTTATC 57.697 45.455 0.00 0.00 0.00 1.75
4110 5185 6.161381 GGAGTTATCCGTTACAAAGAAGTCA 58.839 40.000 0.00 0.00 35.37 3.41
4267 5342 2.424956 GCAATCATCTTCACACTTCCCC 59.575 50.000 0.00 0.00 0.00 4.81
4312 5387 6.543831 GTGTTTCAAGTATAGATCCTGCCATT 59.456 38.462 0.00 0.00 0.00 3.16
4313 5388 6.543465 TGTTTCAAGTATAGATCCTGCCATTG 59.457 38.462 0.00 0.00 0.00 2.82
4314 5389 6.499106 TTCAAGTATAGATCCTGCCATTGA 57.501 37.500 0.00 0.00 0.00 2.57
4315 5390 6.692849 TCAAGTATAGATCCTGCCATTGAT 57.307 37.500 0.00 0.00 0.00 2.57
4316 5391 7.797121 TCAAGTATAGATCCTGCCATTGATA 57.203 36.000 0.00 0.00 0.00 2.15
4317 5392 8.384693 TCAAGTATAGATCCTGCCATTGATAT 57.615 34.615 0.00 0.00 0.00 1.63
4318 5393 9.492730 TCAAGTATAGATCCTGCCATTGATATA 57.507 33.333 0.00 0.00 0.00 0.86
4319 5394 9.761504 CAAGTATAGATCCTGCCATTGATATAG 57.238 37.037 0.00 0.00 0.00 1.31
4320 5395 9.720874 AAGTATAGATCCTGCCATTGATATAGA 57.279 33.333 0.00 0.00 0.00 1.98
4321 5396 9.365906 AGTATAGATCCTGCCATTGATATAGAG 57.634 37.037 0.00 0.00 0.00 2.43
4322 5397 5.954153 AGATCCTGCCATTGATATAGAGG 57.046 43.478 0.00 0.00 0.00 3.69
4323 5398 4.720773 AGATCCTGCCATTGATATAGAGGG 59.279 45.833 0.00 0.00 0.00 4.30
4324 5399 3.874316 TCCTGCCATTGATATAGAGGGT 58.126 45.455 0.00 0.00 0.00 4.34
4325 5400 3.584406 TCCTGCCATTGATATAGAGGGTG 59.416 47.826 0.00 0.00 0.00 4.61
4326 5401 3.341823 CTGCCATTGATATAGAGGGTGC 58.658 50.000 0.00 0.00 0.00 5.01
4327 5402 2.981784 TGCCATTGATATAGAGGGTGCT 59.018 45.455 0.00 0.00 0.00 4.40
4328 5403 3.395607 TGCCATTGATATAGAGGGTGCTT 59.604 43.478 0.00 0.00 0.00 3.91
4329 5404 3.755378 GCCATTGATATAGAGGGTGCTTG 59.245 47.826 0.00 0.00 0.00 4.01
4330 5405 4.330250 CCATTGATATAGAGGGTGCTTGG 58.670 47.826 0.00 0.00 0.00 3.61
4331 5406 4.042062 CCATTGATATAGAGGGTGCTTGGA 59.958 45.833 0.00 0.00 0.00 3.53
4332 5407 5.280882 CCATTGATATAGAGGGTGCTTGGAT 60.281 44.000 0.00 0.00 0.00 3.41
4333 5408 5.489792 TTGATATAGAGGGTGCTTGGATC 57.510 43.478 0.00 0.00 0.00 3.36
4334 5409 3.840666 TGATATAGAGGGTGCTTGGATCC 59.159 47.826 4.20 4.20 0.00 3.36
4335 5410 2.196742 ATAGAGGGTGCTTGGATCCA 57.803 50.000 11.44 11.44 0.00 3.41
4336 5411 1.965414 TAGAGGGTGCTTGGATCCAA 58.035 50.000 25.53 25.53 0.00 3.53
4388 5463 7.747155 AGTCTTTTTAAGAGGCTAAAGTTCC 57.253 36.000 6.60 0.00 38.41 3.62
4389 5464 7.287810 AGTCTTTTTAAGAGGCTAAAGTTCCA 58.712 34.615 6.60 0.00 38.41 3.53
4390 5465 7.778382 AGTCTTTTTAAGAGGCTAAAGTTCCAA 59.222 33.333 6.60 0.00 38.41 3.53
4391 5466 8.076781 GTCTTTTTAAGAGGCTAAAGTTCCAAG 58.923 37.037 6.60 0.00 38.41 3.61
4392 5467 5.959618 TTTAAGAGGCTAAAGTTCCAAGC 57.040 39.130 0.00 0.00 35.47 4.01
4393 5468 3.508845 AAGAGGCTAAAGTTCCAAGCA 57.491 42.857 0.00 0.00 38.01 3.91
4394 5469 2.784347 AGAGGCTAAAGTTCCAAGCAC 58.216 47.619 0.00 2.09 38.01 4.40
4395 5470 1.813178 GAGGCTAAAGTTCCAAGCACC 59.187 52.381 0.00 0.00 38.01 5.01
4396 5471 0.888619 GGCTAAAGTTCCAAGCACCC 59.111 55.000 7.02 0.00 38.01 4.61
4397 5472 0.888619 GCTAAAGTTCCAAGCACCCC 59.111 55.000 0.00 0.00 36.26 4.95
4398 5473 1.547901 GCTAAAGTTCCAAGCACCCCT 60.548 52.381 0.00 0.00 36.26 4.79
4399 5474 2.162681 CTAAAGTTCCAAGCACCCCTG 58.837 52.381 0.00 0.00 0.00 4.45
4400 5475 0.555769 AAAGTTCCAAGCACCCCTGA 59.444 50.000 0.00 0.00 0.00 3.86
4401 5476 0.178990 AAGTTCCAAGCACCCCTGAC 60.179 55.000 0.00 0.00 0.00 3.51
4402 5477 1.062488 AGTTCCAAGCACCCCTGACT 61.062 55.000 0.00 0.00 0.00 3.41
4403 5478 0.690762 GTTCCAAGCACCCCTGACTA 59.309 55.000 0.00 0.00 0.00 2.59
4404 5479 1.073284 GTTCCAAGCACCCCTGACTAA 59.927 52.381 0.00 0.00 0.00 2.24
4405 5480 1.440618 TCCAAGCACCCCTGACTAAA 58.559 50.000 0.00 0.00 0.00 1.85
4406 5481 1.351017 TCCAAGCACCCCTGACTAAAG 59.649 52.381 0.00 0.00 0.00 1.85
4407 5482 1.351017 CCAAGCACCCCTGACTAAAGA 59.649 52.381 0.00 0.00 0.00 2.52
4408 5483 2.616510 CCAAGCACCCCTGACTAAAGAG 60.617 54.545 0.00 0.00 0.00 2.85
4409 5484 1.280457 AGCACCCCTGACTAAAGAGG 58.720 55.000 0.00 0.00 0.00 3.69
4410 5485 1.203313 AGCACCCCTGACTAAAGAGGA 60.203 52.381 0.00 0.00 0.00 3.71
4411 5486 1.208293 GCACCCCTGACTAAAGAGGAG 59.792 57.143 0.00 0.00 0.00 3.69
4412 5487 1.208293 CACCCCTGACTAAAGAGGAGC 59.792 57.143 0.00 0.00 0.00 4.70
4413 5488 1.079658 ACCCCTGACTAAAGAGGAGCT 59.920 52.381 0.00 0.00 0.00 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 1.446618 GGCGGTGGACGTCGTTTAT 60.447 57.895 9.92 0.00 46.52 1.40
254 271 1.441729 GCTAGGTGTGCCATCGCTA 59.558 57.895 0.00 0.00 37.19 4.26
410 467 1.115467 CCTGCACCTCTAGATCCGTT 58.885 55.000 0.00 0.00 0.00 4.44
443 500 3.399181 GTCCCTGGCATGTCGGGA 61.399 66.667 27.30 23.81 44.52 5.14
476 553 3.712907 GCCACCCAAGCTCCCGTA 61.713 66.667 0.00 0.00 0.00 4.02
704 833 5.048364 TGGTCCGATCACAAAAATTCGATTT 60.048 36.000 0.00 0.00 33.59 2.17
705 834 4.457603 TGGTCCGATCACAAAAATTCGATT 59.542 37.500 0.00 0.00 33.59 3.34
721 850 2.654289 CGTGTGTGGATGGTCCGA 59.346 61.111 0.00 0.00 40.17 4.55
728 857 0.249699 TCTCAAACGCGTGTGTGGAT 60.250 50.000 27.65 0.00 33.85 3.41
732 861 3.305623 CGTCTCAAACGCGTGTGT 58.694 55.556 27.65 6.93 45.76 3.72
740 869 2.095718 GCACCTCAAATCCGTCTCAAAC 60.096 50.000 0.00 0.00 0.00 2.93
759 888 6.271624 ACCTAAAACTTAACTCCTAAGAGGCA 59.728 38.462 0.00 0.00 45.11 4.75
766 895 5.164897 ACCCCACCTAAAACTTAACTCCTA 58.835 41.667 0.00 0.00 0.00 2.94
810 948 0.545646 GCATCTCTTGCCCTTCTCCT 59.454 55.000 0.00 0.00 46.15 3.69
998 1144 4.553668 GCCTGCTGCTCATCATGA 57.446 55.556 0.00 0.00 36.87 3.07
1635 1781 4.752879 TAGTGCTTGGCGGCGGAC 62.753 66.667 9.78 2.03 34.52 4.79
1978 2153 0.249238 GAACACCATTGCAACGCCAA 60.249 50.000 0.00 0.00 0.00 4.52
1983 2158 2.483877 TCTGATCGAACACCATTGCAAC 59.516 45.455 0.00 0.00 0.00 4.17
2023 2198 2.493675 ACGTCATGTATCTGCAGTCTGT 59.506 45.455 14.67 1.37 0.00 3.41
2079 2254 1.200519 CAGAACCGGATCTTGGGGTA 58.799 55.000 12.21 0.00 32.68 3.69
2080 2255 0.840722 ACAGAACCGGATCTTGGGGT 60.841 55.000 12.21 4.01 34.99 4.95
2081 2256 0.392998 CACAGAACCGGATCTTGGGG 60.393 60.000 12.21 3.33 0.00 4.96
2096 2271 6.646240 CCCAAACAGGAAACAATTATTCACAG 59.354 38.462 5.75 0.00 41.22 3.66
2380 2558 3.760684 GGCCAACTTCTTGAACTGATCAT 59.239 43.478 0.00 0.00 38.03 2.45
2447 2855 8.500753 ACATCATTAAAATACTCGCTAAACCA 57.499 30.769 0.00 0.00 0.00 3.67
2508 3515 4.946784 ATTGCGGACAGTTGAGAATTAC 57.053 40.909 0.00 0.00 0.00 1.89
2519 3526 7.697691 ACTAGATTTATGAAAATTGCGGACAG 58.302 34.615 0.00 0.00 35.41 3.51
2653 3676 3.063452 GCACATAGAATTACCGGTGTGTG 59.937 47.826 19.93 18.84 39.19 3.82
2766 3789 1.929169 CGTACTACGTCAGATCGACCA 59.071 52.381 0.00 1.39 42.07 4.02
2780 3803 6.735145 GCGGTACTCCTAGTAGTTACGTACTA 60.735 46.154 11.22 0.00 38.33 1.82
2781 3804 5.593010 CGGTACTCCTAGTAGTTACGTACT 58.407 45.833 0.00 0.00 41.04 2.73
2782 3805 4.209495 GCGGTACTCCTAGTAGTTACGTAC 59.791 50.000 11.22 2.60 30.12 3.67
2803 3826 4.034858 ACATCATGTTAATTGAGCTGAGCG 59.965 41.667 0.00 0.00 0.00 5.03
2953 3987 4.142049 TGTTGGCTGATCATATACACGTCA 60.142 41.667 0.00 0.00 0.00 4.35
3050 4084 0.299895 CGTTGTCGATCTCATGCTGC 59.700 55.000 0.00 0.00 39.71 5.25
3051 4085 0.926155 CCGTTGTCGATCTCATGCTG 59.074 55.000 0.00 0.00 39.71 4.41
3052 4086 0.807667 GCCGTTGTCGATCTCATGCT 60.808 55.000 0.00 0.00 39.71 3.79
3053 4087 1.638467 GCCGTTGTCGATCTCATGC 59.362 57.895 0.00 0.00 39.71 4.06
3054 4088 1.482621 CCGCCGTTGTCGATCTCATG 61.483 60.000 0.00 0.00 39.71 3.07
3055 4089 1.226974 CCGCCGTTGTCGATCTCAT 60.227 57.895 0.00 0.00 39.71 2.90
3226 4260 2.099263 GTCATCATGAAATGCTGCTGCT 59.901 45.455 17.00 0.00 46.21 4.24
3227 4261 2.460918 GTCATCATGAAATGCTGCTGC 58.539 47.619 8.89 8.89 46.21 5.25
3228 4262 2.688446 AGGTCATCATGAAATGCTGCTG 59.312 45.455 0.00 0.00 46.21 4.41
3293 4339 1.210155 GCACGACAAGATGTTGCCC 59.790 57.895 1.83 0.00 35.14 5.36
3326 4372 3.527427 TGGCGACGCTGATCCGAT 61.527 61.111 20.77 0.00 0.00 4.18
3344 4390 2.805353 CTGTCGCCGTCGTTCTGG 60.805 66.667 0.00 0.00 36.96 3.86
3533 4579 1.701847 CTCCATATGCCCAGCCTAGTT 59.298 52.381 0.00 0.00 0.00 2.24
3546 4592 7.127032 ACGTACCCTACTAGCTATACTCCATAT 59.873 40.741 0.00 0.00 0.00 1.78
3547 4593 6.441924 ACGTACCCTACTAGCTATACTCCATA 59.558 42.308 0.00 0.00 0.00 2.74
3618 4666 5.659463 ACAATTAAAAACACAGCAAGCAGA 58.341 33.333 0.00 0.00 0.00 4.26
3650 4698 8.876181 AGTACATACACTATTGCCCATTGTATA 58.124 33.333 0.00 0.00 32.77 1.47
3661 4726 6.980978 AGCAAGCAGTAGTACATACACTATTG 59.019 38.462 2.52 2.46 40.09 1.90
3786 4852 6.215121 TCCTCAACAAGTTTGCAATAACATG 58.785 36.000 0.00 2.20 34.02 3.21
3903 4973 7.678947 ATGAAGACCTAAAAACTCATGTCAG 57.321 36.000 0.00 0.00 0.00 3.51
3904 4974 8.463930 AAATGAAGACCTAAAAACTCATGTCA 57.536 30.769 0.00 0.00 0.00 3.58
3967 5042 5.181245 ACTTCATTTGACGACGAATCCAAAT 59.819 36.000 0.00 8.79 39.10 2.32
3977 5052 4.748102 TGGTTAGACACTTCATTTGACGAC 59.252 41.667 0.00 0.00 0.00 4.34
4052 5127 6.430925 GGTTTATTAGTCGGGTACAGGTTTTT 59.569 38.462 0.00 0.00 0.00 1.94
4058 5133 4.741321 TGGGTTTATTAGTCGGGTACAG 57.259 45.455 0.00 0.00 0.00 2.74
4061 5136 3.843027 TGGTTGGGTTTATTAGTCGGGTA 59.157 43.478 0.00 0.00 0.00 3.69
4083 5158 6.210984 ACTTCTTTGTAACGGATAACTCCTCT 59.789 38.462 0.00 0.00 39.65 3.69
4267 5342 1.081892 CACGAGGTCCTTGCTTCATG 58.918 55.000 5.98 0.00 0.00 3.07
4312 5387 3.840666 GGATCCAAGCACCCTCTATATCA 59.159 47.826 6.95 0.00 0.00 2.15
4313 5388 3.840666 TGGATCCAAGCACCCTCTATATC 59.159 47.826 13.46 0.00 0.00 1.63
4314 5389 3.874316 TGGATCCAAGCACCCTCTATAT 58.126 45.455 13.46 0.00 0.00 0.86
4315 5390 3.344535 TGGATCCAAGCACCCTCTATA 57.655 47.619 13.46 0.00 0.00 1.31
4316 5391 2.196742 TGGATCCAAGCACCCTCTAT 57.803 50.000 13.46 0.00 0.00 1.98
4317 5392 1.839994 CTTGGATCCAAGCACCCTCTA 59.160 52.381 35.47 8.33 45.38 2.43
4318 5393 0.622665 CTTGGATCCAAGCACCCTCT 59.377 55.000 35.47 0.00 45.38 3.69
4319 5394 3.181526 CTTGGATCCAAGCACCCTC 57.818 57.895 35.47 0.00 45.38 4.30
4326 5401 7.283354 GACTAAAATAAGTCCCTTGGATCCAAG 59.717 40.741 37.68 37.68 42.72 3.61
4327 5402 7.036863 AGACTAAAATAAGTCCCTTGGATCCAA 60.037 37.037 25.53 25.53 45.86 3.53
4328 5403 6.447084 AGACTAAAATAAGTCCCTTGGATCCA 59.553 38.462 11.44 11.44 45.86 3.41
4329 5404 6.768381 CAGACTAAAATAAGTCCCTTGGATCC 59.232 42.308 4.20 4.20 45.86 3.36
4330 5405 7.496263 GTCAGACTAAAATAAGTCCCTTGGATC 59.504 40.741 0.00 0.00 45.86 3.36
4331 5406 7.182930 AGTCAGACTAAAATAAGTCCCTTGGAT 59.817 37.037 0.00 0.00 45.86 3.41
4332 5407 6.500751 AGTCAGACTAAAATAAGTCCCTTGGA 59.499 38.462 0.00 0.00 45.86 3.53
4333 5408 6.712276 AGTCAGACTAAAATAAGTCCCTTGG 58.288 40.000 0.00 0.00 45.86 3.61
4334 5409 9.720769 TTTAGTCAGACTAAAATAAGTCCCTTG 57.279 33.333 26.93 0.00 44.84 3.61
4362 5437 9.451002 GGAACTTTAGCCTCTTAAAAAGACTAT 57.549 33.333 2.82 0.00 33.98 2.12
4363 5438 8.434392 TGGAACTTTAGCCTCTTAAAAAGACTA 58.566 33.333 2.82 0.00 33.98 2.59
4364 5439 7.287810 TGGAACTTTAGCCTCTTAAAAAGACT 58.712 34.615 2.82 0.00 33.98 3.24
4365 5440 7.506328 TGGAACTTTAGCCTCTTAAAAAGAC 57.494 36.000 2.82 0.00 33.98 3.01
4366 5441 7.255486 GCTTGGAACTTTAGCCTCTTAAAAAGA 60.255 37.037 2.82 0.00 33.98 2.52
4367 5442 6.863645 GCTTGGAACTTTAGCCTCTTAAAAAG 59.136 38.462 0.00 0.00 35.54 2.27
4368 5443 6.322712 TGCTTGGAACTTTAGCCTCTTAAAAA 59.677 34.615 0.00 0.00 34.03 1.94
4369 5444 5.830991 TGCTTGGAACTTTAGCCTCTTAAAA 59.169 36.000 0.00 0.00 34.03 1.52
4370 5445 5.240844 GTGCTTGGAACTTTAGCCTCTTAAA 59.759 40.000 0.00 0.00 34.03 1.52
4371 5446 4.760204 GTGCTTGGAACTTTAGCCTCTTAA 59.240 41.667 0.00 0.00 34.03 1.85
4372 5447 4.324267 GTGCTTGGAACTTTAGCCTCTTA 58.676 43.478 0.00 0.00 34.03 2.10
4373 5448 3.149981 GTGCTTGGAACTTTAGCCTCTT 58.850 45.455 0.00 0.00 34.03 2.85
4374 5449 2.553247 GGTGCTTGGAACTTTAGCCTCT 60.553 50.000 0.00 0.00 34.03 3.69
4375 5450 1.813178 GGTGCTTGGAACTTTAGCCTC 59.187 52.381 0.00 0.00 34.03 4.70
4376 5451 1.547901 GGGTGCTTGGAACTTTAGCCT 60.548 52.381 0.00 0.00 34.03 4.58
4377 5452 0.888619 GGGTGCTTGGAACTTTAGCC 59.111 55.000 0.00 0.00 34.03 3.93
4378 5453 0.888619 GGGGTGCTTGGAACTTTAGC 59.111 55.000 0.00 0.00 35.50 3.09
4379 5454 2.162681 CAGGGGTGCTTGGAACTTTAG 58.837 52.381 0.00 0.00 0.00 1.85
4380 5455 1.777878 TCAGGGGTGCTTGGAACTTTA 59.222 47.619 0.00 0.00 0.00 1.85
4381 5456 0.555769 TCAGGGGTGCTTGGAACTTT 59.444 50.000 0.00 0.00 0.00 2.66
4382 5457 0.178990 GTCAGGGGTGCTTGGAACTT 60.179 55.000 0.00 0.00 0.00 2.66
4383 5458 1.062488 AGTCAGGGGTGCTTGGAACT 61.062 55.000 0.00 0.00 0.00 3.01
4384 5459 0.690762 TAGTCAGGGGTGCTTGGAAC 59.309 55.000 0.00 0.00 0.00 3.62
4385 5460 1.440618 TTAGTCAGGGGTGCTTGGAA 58.559 50.000 0.00 0.00 0.00 3.53
4386 5461 1.351017 CTTTAGTCAGGGGTGCTTGGA 59.649 52.381 0.00 0.00 0.00 3.53
4387 5462 1.351017 TCTTTAGTCAGGGGTGCTTGG 59.649 52.381 0.00 0.00 0.00 3.61
4388 5463 2.616510 CCTCTTTAGTCAGGGGTGCTTG 60.617 54.545 0.00 0.00 28.24 4.01
4389 5464 1.630878 CCTCTTTAGTCAGGGGTGCTT 59.369 52.381 0.00 0.00 28.24 3.91
4390 5465 1.203313 TCCTCTTTAGTCAGGGGTGCT 60.203 52.381 0.00 0.00 35.61 4.40
4391 5466 1.208293 CTCCTCTTTAGTCAGGGGTGC 59.792 57.143 0.00 0.00 35.61 5.01
4392 5467 1.208293 GCTCCTCTTTAGTCAGGGGTG 59.792 57.143 0.00 0.00 35.61 4.61
4393 5468 1.079658 AGCTCCTCTTTAGTCAGGGGT 59.920 52.381 0.00 0.00 35.61 4.95
4394 5469 1.872773 AGCTCCTCTTTAGTCAGGGG 58.127 55.000 0.00 0.00 35.39 4.79


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.